Harnessing the New Sciences for Crop Improvement

- Agriculture in the developing world: Connecting innovations in plant research to downstream applications

Agriculture will never truly thrive in places like
subSaharan Africa unless solutions are found for fundamental issues,
such as lack of roads, weak input and output markets, the low level of
general health and education of poor farmers, poorly functioning
extension services, and gender inequity that places a disproportionate
burden on women in agriculture, all critical issues that cannot be
solved by biotechnology and are well beyond the scope of this article.
Even in the specific area of crop improvement, there are great
opportunities to apply conventional breeding that do not need to draw
on the very latest discoveries in plant biology. One of the first rules
of our Food Security Team at the Rockefeller Foundation is, “If the
breeders can solve the problem, let them do it.” In places like
subSaharan Africa, once breeders began tailoring their efforts to
breeding targeted specifically to African conditions, it became
apparent that significant crop improvement is possible through
conventional approaches (11).

The Increasing Power of Molecular Breeding.
With respect to the recent advances in the plant sciences, as the
sequences of many plant genomes become known, the power of genomics for
applied breeding has to be one of the most exciting advances of recent
years. Extremely valuable to breeders in the national agricultural
research systems is the ability to genotype their collections to get a
clear picture of their diversity and how such diversity might be
enhanced through sharing and access to global collections. The use of
marker-assisted selection in cases where phenotyping presents a
challenge or to trace introgression of known genes or important regions
from wild relatives should also become part of every serious national
breeding program.

Complete sequence information, maps, and a huge array of molecular markers exist for rice; with more sequence information
for other crops, new techniques for assessing allelic diversity, and a better understanding of synteny (12),
these are now being adapted for the breeding of other crops. Yet, for
orphan crops like cowpea, common bean, the millets, tef, and cassava,
we still have insufficient numbers of ESTs, bacterial artificial
chromosome libraries, molecular maps, and markers (13). Programs such as the Generation Challenge Program and crop-specific initiatives such as Phaseomics are beginning to address
these limitations, but a glance at the number of ESTs available for different organisms (www.ncbi.nlm.nih.gov/dbEST/dbEST_summary.html)
indicates that more funds and efforts are clearly warranted. Good value
can also be had through sequencing of the genomes of major plant
pathogens. In addition, there are many challenges in creating the
needed infrastructure, including high-throughput analysis systems and
critical high-speed Internet access to the tools of bioinformatics;
development of a pool of breeders well-versed in the use of these tools
also still limits progress on this front. Networks in Asia that brought
together rice (the Asian Rice Biotechnology Network, ARBN) and maize
breeders (the Asian Maize Biotechnology Network, AMBIONET) to build
capacity and better interactions among molecular breeders have been
most successful; a similar fledgling network called AMMANET (African
Molecular Marker Applications Network), which holds promise for African
breeders, is another welcome development.

A
new regional center in Nairobi called Biosciences for East and Central
Africa (BECA) is intended to serve as a center of excellence for
agricultural biotechnology that will interact with and serve the
various universities and national agricultural research systems of the
region. At BECA, the modern tools of genomics can be shared with
breeding programs through training, provision of markers,
high-throughput analysis coupled with a sophisticated bioinformatics
platform, and joint efforts to genotype key crops and identify projects
suitable for marker-assisted selection. For example, a recent meeting
at BECA brought together 28 sorghum and millet breeders from national
agricultural research systems representing 14 countries of the region
and specialists in molecular breeding and genomics from the U.S.,
Europe, and the International Crops Research Institute for the
Semi-Arid Tropics (ICRISAT). The purpose of the meeting was to learn
about the genomics tools available to them from both public and private
sources and to discuss and draft project proposals for application of
marker-assisted selection in African sorghum and millet breeding
programs. More extensive promotion of such collaborations and other
forms of imaginative human capacity building is clearly warranted.

The use of molecular markers has helped highlight the importance of genes from wild relatives for use in crop improvement
(14, 15) and, as evidenced by recent work on tomato improvement, the results can sometimes be spectacular (16). African farmers are showing real enthusiasm for new interspecific hybrids that combine the best of both Asian and African
rices (17).
For complex traits, the identification of quantitative trait loci (QTL)
has advanced to a considerable degree, to the point where it is now
becoming somewhat more feasible to identify specific genes that control
the traits underlying the QTL (e.g., see ref. 18
and refs. therein). Advances in genomics should also be able to
contribute new insights to our currently vague understanding of that
most important of traits, heterosis (hybrid vigor). Can the recent work
showing how inbred lines of maize differ strikingly in gene sequences
(e.g., ref. 19) and gene expression patterns (20)
provide some clues? Can such understanding help us determine whether
there is good value in promoting the development of hybrid sorghum and
millets for Africa and to explore further the potential of heterosis in
many crops beyond maize? Certainly, development of hybrid seed is one
way to promote viable seed markets for crops. But do we understand well
enough the cost–benefit equations for small farmers with respect to
purchase of high-quality seed (hybrid or not) vs. the saving of seed,
and is the development of a strong private-sector seed business a
necessary part of moving such farmers beyond the subsistence level?
Such questions go beyond the realm of science into that of sociology
and economics, but good answers clearly require input from the
scientific community.

Are GM Crops the Answer?
A fierce debate continues over the potential of GM crops to solve the
problems of hunger in the developing world. At one extreme, proponents
argue that these new technologies will be the panacea needed to solve
hunger, whereas the other extreme argues that the technologies are
unsafe to both humans and the environment and are being promoted simply
as a means to further the interests of the large multinational
companies that market them. Those arguments are not the focus of this
article, except to say that most reasonable people understand the truth
lies somewhere between these extremes and, at best, GM crops are only
one of many approaches available to solve world hunger, and developing
countries should be free to assess their worth within the context of
their own needs and priorities. It can be argued that all new advances,
including the undoubted success of the Green Revolution, can have their
downsides. A recent example is the Roundup Ready soybean, which has
been a huge success for the farmers of Argentina and Brazil but may be
promoting a debatably dangerous trend toward monoculture and expansion
of farming into valuable sites for biodiversity. Whatever one's opinion
on these issues, there seems to be little doubt that the endless, and
often shrill, GM debate has limited the development of crops that could
be very relevant to poor farmers by reducing the number of donors
willing to support such efforts, raising concerns over liability in
companies considering the provision of their technologies for use in
public-sector projects and creating confusion and uncertainty about
whether to allow even simple testing of the efficacy of new transgenic
crops in developing world countries. A key consequence of this debate
has been to lower the level of engagement of skilled scientists in key
laboratories who should be building better capacity in this field.

Most
of the discussions on GM crops are much too narrowly framed and focus
just on the current situation, wherein only four major GM crops, with
only two traits, represent the bulk of the GM market today. These
traits are insect and/or herbicide resistance in soybeans, maize,
canola, and cotton, a very limited repertoire that was designed by the
private sector for use in large-scale agriculture. First, I shall
discuss the extent to which this limited repertoire may be suitable and
beneficial for use in the developing world. Then I shall make the
argument that there are many other opportunities for crop improvement
besides the current GM crops that could be developed by taking a more
imaginative look at the recent advances in gene discovery.

The Relevance of Current GM Traits and Crops for the Developing World.
In subSaharan Africa, maize is clearly the major staple human food crop
in many countries, and cotton is grown as a commercial crop even by the
poor in countries like Mali, South Africa, India, and China. For these
crops, a strong commercial market for GM seed is developing that, at
least in principle, targets both large- and small-scale farmers.
Accumulating evidence indicates that the current GM crops can clearly
prove beneficial to small as well as large farmers. Varieties of cotton
with the toxin gene from Bacillus thuringiensis (Bt) are proving their worth to poor farmers in South Africa (21) as well as parts of Asia (22, 23), and Bt rice is performing well in late-stage trials in China (24).
The benefits of these crops can be quite different depending upon
circumstances. In China, where yields of conventional cotton and rice
are maintained through heavy use of pesticides, the benefits are in
savings on the costs of these inputs and on the health of workers from
pesticide poisoning and protection of the environment through the use
of fewer chemicals. In South Africa and India, where costs of
pesticides are prohibitive for the poorest farmers, the benefits are
more clearly seen in substantial yield increases when pests are
controlled through Bt
technology. However, quite worrisome for the developing world is the
serious issue of illegal seed movement and/or sales for GM crops, which
occur widely in countries like Brazil, India, and China, which has
lowered the incentive of the private sector to continue their
involvement, weakened the private seed sector within these countries,
and also lowered the quality of seed available to farmers (e.g., see
ref. 25).

In contrast to Bt,
where the trait is embedded in the seed, herbicide tolerance is a trait
more beneficial to large-scale farmers who can afford to buy chemical
inputs. Yet, several developments may require some rethinking of this
belief. One of these is the increasing shift in Asia from growing rice
in paddies that provide good weed control to aerobic conditions. In
Africa, cost considerations, as well as the variety of crops grown on a
single small plot, make the idea of herbicide tolerance seem less
attractive for small-scale farmers. Yet, as shown in Argentina,
herbicide-tolerant crops certainly favor the development of no-till
agriculture, which can control erosion, save water, and sometimes allow
for double-cropping; furthermore, in Africa, hand-weeding occupies much
of a farmer's time and, with the severe labor shortages developing as a
result of the HIV/AIDS epidemic, the science community should perhaps
think about promoting cropping systems that save the time and energy of
the farmer.

All
these facts indicate there definitely can be a positive role for the
private sector for the sale of seed for these major crops with these
traits in at least some areas of the developing world. Experience tells
us that if farmers benefit, if they have the cash, or if they can be
helped through microcredit schemes, and if strong regulatory systems
are in place (as in the U.S., Argentina, and South Africa), they will
buy such quality seed. But if governments, as was the case in Brazil
with the Roundup Ready soybean, delay approval of a GM crop that
farmers clearly want, the farmers often find a way to get it illegally,
compromising both the quality of seed available, the viability of
private seed sector, and the ability of a government to provide
adequate regulation.

In
terms of strategy, one has to strongly question whether the public
sector should waste its precious resources developing any product that
duplicates what the private sector can make available. However, similar
benefits could be imagined for these same traits in a number of crops
that are traditionally outside the formal seed sector and of no
interest to the large private-sector companies. Targets where Bt genes could
potentially be used to address the constraints of poor farmers include
the pod borers that attack cowpea and pigeon pea; the stem borers of
rice, weevils, and/or nematodes that attack banana or sweet potato; the
diamondback moth that affects cabbage; or the fruit and shoot borers of
eggplant. For maize, the larger grain borer has become a serious
storage pest for maize in Eastern Africa and is a target trait not
likely to be addressed by the private sector (26).
Techniques now exist for transformation of all of these crops, although
some would certainly benefit from further optimization. Genes have
clearly been identified to control most Lepidopteran pests such as the
moths and pod, stem, and fruit borers. Searches are still ongoing to
identify the most effective Bts that may control Coleopteran pests like large grain borer, weevils, and nematodes; these are cases where the application
of gene shuffling techniques may be important for enhancing effectiveness.

Moving Beyond Bt and Herbicide Tolerance.
The plant science community is discovering a vast array of genes that
control all aspects of plant growth and development. Although GM crops
based on many of these other genes may have little or no commercial
potential, they can have a much different value when considered for
certain crops important to the developing world. The creation of
nutritionally enhanced crops such as Golden Rice is an obvious example (27, 28),
but it should be possible also to enhance mineral content and improve
the digestibility of crops like sorghum and to eliminate toxic
compounds such as the cyanogenic glycosides of cassava. Although
perhaps not quite ready for downstream application, the recent work on
the identification of new genes that control phosphorous utilization or
tolerance to aluminum offers future promise (7). Also worthy of more intense study are the arbuscular mycorrhizal fungi that form symbiotic relationships with >80% of all
plant species and certainly contribute to the more efficient extraction of nutrients from the soil (29).
A major problem in working with these has been the inability to culture
these fungi in the absence of the host; in this regard, an exciting
breakthrough is the recent identification of strigolactones as key
stimulants of fungal development, which are secreted from plant roots
in response to low phosphate; this work may also have significance for
research on the parasitic weed Striga, because similar compounds also
stimulate Striga seed germination (29, 30).

Through the classic studies of coat-protein-mediated resistance (31) and, more recently, using RNA interference, we know it is entirely feasible to control RNA viruses such as ringspot, which
attacks papaya (32);
similar approaches can potentially be used with great benefit for the
brown streak virus of cassava or against cucumber mosaic virus, which
affects many vegetable crops. The ssDNA geminiviruses that cause
devastating diseases of cassava, maize, banana, and tomato, because
they do not involve an RNA-based intermediate for replication, were
thought not to be controllable by this approach, but recent evidence
suggests they may nevertheless be targets for posttranscriptional gene
silencing (33); other targets for control are also being explored (e.g., refs. 34 and 35).

Bacterial and fungal diseases represent an enormous challenge, because they cause such huge losses to farmers who lack the
labor and skills needed for good field management and the money for effective pesticides (36).
Breeding for resistance can clearly solve some of these problems, but
development of pathogen resistance is a persistent problem, so the
plant community needs to unite to come up with more and better
strategies to achieve durable forms of resistance, a goal I would list
as one the highest priorities for future plant research for the
developing world.

I
think there is no field in plant biology that has a collection of more
imaginative scientists than those who have discovered such an amazing
amount of information about pathways invoked upon the response of
plants to pathogens or insects. Surely the field can benefit from
continued work on the complex events involved in early recognition,
including further identification of interacting proteins and the role
of proteolysis in the process (37, 38), and on the connections between and relative importance of basal and induced defense systems (38). For both breeding and transgenic approaches that target resistance (R) or avirulence (AVR) genes, a clearer understanding of the nature of the fitness costs of both the R genes of the plant (39) and AVR genes in the pathogen (40) is one avenue worthy of additional exploration. It is clear that the simple idea of constitutive overexpression of key genes
in resistance pathways often leads to loss of plant vigor and yield penalties (41).
At first glance, the idea of inducible overexpression of key
transcription factors that control a range of downstream responses
seems attractive for disease resistance (42) and may represent one of the best approaches for other complex traits, such as drought tolerance (43).
Equally critical to the success of this approach would seem to be the
type of promoter selected. Unfortunately, for all transgenic work, the
pubic sector is woefully lacking in a suite of good promoters for both
eudicot and monocot species that are tissue-specific, developmentally
regulated, and/or inducible by environmental cues like stress, disease,
or cheap and safe chemicals. But the use of transcription factors for
the control of diseases may be more problematic than originally
imagined because of the complexity of the response pathways and the
discovery of negative crosstalk that sometimes occurs between the
salicylic acid-regulated pathway for disease resistance and the
jasmonate–ethylene-regulated pathways important for insect resistance (44). One key regulator that intersects both of these pathways is the NPR1 gene (45);
understanding ways to modulate its location and/or function in either
pathway might therefore provide one way to control at least one type of
negative crosstalk. Yet this is one field where it seems the more we
learn, the more complicated the challenge, and one longs for another
magic bullet similar to the Bt genes that control insects so well and
so durably. Perhaps scientists need to think more about creating,
through molecular design, some imaginative killer genes like Bt that
could target specific groups of plant pathogens.

We
should also be able to draw on the fascinating findings from the world
of plant development to improve certain crops. At the meeting that
brought together bench and field scientists, breeders told molecular
biologists that cassava is very poor at flowering and, even worse, two
varieties one wants to cross often do not flower at the same time in
the same breeding station. From this emerged a project to attempt to
create cassava for breeding purposes that has a flower-inducing gene
under the control of an ethanol-inducible promoter. Ideas also emerged
for projects that could aim to dwarf the ungainly East African Highland
Banana or the favorite cereal crop of Ethiopia called tef, to enhance
drought tolerance through stress-induced changes in root architecture,
and to ask whether RNA interference technology might be used to control
the parasitic weed Striga by sending, through host–parasite
connections, an engineered small RNA from maize to directly target a
critical Striga gene. References too numerous to cite here indicate we
now should be able, perhaps with single-gene changes, to control traits
like tillering in cereals; alter root or shoot branching patterns;
control the timing and extent of flowering and/or alter vernalization
requirements; change seed size or number; control seed shattering; and
perhaps even think about altering flower color, scent, structure,
and/or time of opening to prevent gene flow by pollinating insects. In
Africa, children are made to stay home from school to scare away the
birds that steal exposed grains of crops like sorghum; perhaps a mutant
gene like “Tassel Sheath” of maize might be transferred to sorghum to
mimic the advantages found in the enclosed grain of maize. Finally, the
new insights emerging daily on how microRNAs control development (46)
should offer many other new approaches to changing plant form and
function. The above are only some examples of what might be done today,
given current technologies, and only hint at what might be done in the
future when additional insights become available, although they do not
take into account cost–benefit analyses for any given projects or other
roadblocks that might need to be considered.

One recent impressive tour de force study with rice involving genes controlling development is instructive for the current debate about whether molecular breeding
should be favored over a transgenic approach. Using all the tools of modern breeding, Ashikari et al. (18) identified a strong quantitative trait locus (QTL) that controls grain number, cloned the gene (a cytokinin oxidase) in
an effort that involved the analysis of 13,000 F2
plants, and created transgenic plants with a larger grain number by
overexpression of the gene. Having learned much about this gene and its
relationship to other members of the same gene family through the
transgenic approach, the authors (18) then returned to breeding to pyramid the locus for an enhanced grain number with that surrounding the semidwarf gene (sd1), resulting in a plant that should substantially enhance grain yield. Ashikari et al. (18)
have impressively shown what can be accomplished through molecular
breeding, particularly as one approach to the identification of
candidate genes; however, one has to ask whether, once specific genes
are identified (as they were for both the cytokinin oxidase and the
dwarfing gene), it would not make more sense to pursue a targeted
transgenic approach for pyramiding the genes. In the end, the goals of
breeding and transgenic research are the same, the introgression of
good alleles for crop improvement. With breeding, linkage
disequilibrium is a reality that often (but certainly not always) can
result in the transfer of unfavorable genes along with the targeted
good gene, whereas the transgenic approach eliminates this problem.
Once candidate genes (and/or or key alleles of promoters of genes) are
verified for traits of interest, either through QTL or functional
genomics approaches, it would seem the most obvious route for trait
improvement should be to move each good allele (and, if two or more,
preferably linked to each other) selectively to the crop. Even from a
regulatory point of view, this should be more attractive, because one
knows exactly what is being transferred. Unfortunately, under the
current regulatory climate, any new variety containing one or two new
genes produced through breeding can find an easy path to approval and
release, whereas the same variety with the very same new genes produced
through transgenic approaches may be held up for years, if not forever,
awaiting the approvals necessary for release to farmers.